Syllabus

Syllabus

Syllabus

Extended Syllabus

Extended Syllabus PDF

Book

The Book of R - PDF

WebPage

Course Home Page LINK

Week 1 - Presentation LINK

Good News

DataCamp - LINK

DataCamp

DataCamp

The Value of DataCamp Class

• 1 $ -> 8 TL

• Standard -> 12$ / month

• Course -> 6 month

• People -> 30

8 TL * 12$ * 6 month * 30 people

17.280 TL

DataCamp

Filtered course for R -> 147 courses

We will have new assignments

What is Unix?

• UNIX is a computer operating system.
• It was first developed in 1969 at Bell Labs (USA).
• In 1972, the Unix code was rewritten with the new C programming language (unix philosophy).

(Dennis, Ken, PDP-11 (16-bit), 1970)

What is Unix Philosophy?

The Unix philosophy emphasizes building simple, short, clear, modular, and extensible code that can be easily maintained and repurposed by developers other than its creators.

• Multi-user and parallel computing
• Adaptable with all computers

Ken Thompson and Dennis Ritchie , 1973

What is GNU?

• A wildebeest (or gnu) is an animal. Lives in Africa.
• GNU is the name of a computer operating system.
• The GNU project was started by Richard Stallman in 1983.
• GNU’s Not Unix!
• Fully free to modify, share and publish.

Conference: “Free Software: Human Rights in Your Computer”, 2014

GNU Kernel

• Richard Stallman; American free software movement activist and programmer.
• GNU is a project to create an operating system, wholly free software.

• GNU’s own kernel (GNU Hurd) was not ready.
• The only major component missing was the kernel.

What is Linux (or GNU/Linux) ?

• Linux (or GNU/Linux) is a Unix-like operating system.
• GNU did not have all the parts.
• The kernel (GNU Hurd) is not yet completely built.
• In 1991 Linus Torvalds began to work -> Linux kernel.

Linux kernel completed GNU tools. These operating systems popularly known as Linux.

Unix VS Linux?

• Linux does not use code from UNIX.

• The idea and names of commands are similar.

GNU/Linux Distributions

Linux_Distribution_Timeline

Terminal

A computer terminal is a hardware device that is used for entering data into, and displaying or printing data from a computer or a computing system.

Terminal

We are looking at inside of a folder.

(with ls command)

Terminal and a folder window

Terminal

When you open the Terminal then you are in the shell.

You can write command, talk with the kernel and application

Like an interface for shell

Why Terminal

• Connect to remote computer or machine (supercomputer or Network-attached storage (NAS) )

• Operating system without screen
• Or when you can not use your mouse

Basic GNU/Linux Commands

• Frequently Used Terms

• Directory Commands

• File Commands

• Special Commands

• vi Editor, Print Commands and Symbols

Frequently Used Terms

• File and Folder
• Directory
  • Parent Directory
  • Working Directory
• User
• Root or Root Directory
• Environments
• Backup
• Command, Command Line, Console
• Warning, Error, Permission Denied
• Segmentation Fault

Frequently Used Terms

• File and Folder
• Directory Path, Parent and Working Directory

Frequently Used Terms

• File and Folder
• Directory Path, Parent and Working Directory

Frequently Used Terms

User, Root and Home Directory

whoami

## emirtoker

Root directory symbol; “/”. Home directory symbol; “~”.

Frequently Used Terms

Environments and Backup

printenv  

Helps to the processes (codes, packages, softwares)

Frequently Used Terms

Command Line, Command

or just shell

Frequently Used Terms

Warning, Error, Permission Denied, Segmentation Fault

Or Fatal Error

Directory Commands

• pwd (Print Working Directory)

• ls (List Directories)

• cd (Change Directory)

• mkdir (Make Directory)

Directory Commands - pwd

(Print Working Directory)

pwd

## /Users/emirtoker/Desktop/Memurluk/Software_Tools_for_Earth_&_Environmental_Science/Software_Tools_R_Github/Presentation

Directory Commands - ls

(List Files/Directories)

ls

## 18397_Cekmekoy_Omerli.csv
## 18397_Cekmekoy_Omerli.xlsx
## 18397_Cekmekoy_Omerli_15dk.txt
## Assessment_Test.Rmd
## Assessment_Test.html
## CPC.png
## Final_Project.Rmd
## Final_Project.html
## Final_Project.pdf
## Int_wp.png
## Int_wp_00.png
## Mean_plot.png
## MidTerm_Project.Rmd
## MidTerm_Project.html
## MidTerm_Project.pdf
## MidTerm_Project_Emir.Rmd
## MidTerm_Project_Emir.html
## MidTerm_Project_Emir.pdf
## Pdf_Week5_-_R_Language_Part_1.Rmd
## Pdf_Week5_-_R_Language_Part_1.pdf
## Pdf_Week5_-_R_Language_Part_1_files
## Presentation.Rproj
## Presentation_Week10_-_R_Programming_Part_2.Rmd
## Presentation_Week10_-_R_Programming_Part_2.html
## Presentation_Week11_-_R_Statistics.Rmd
## Presentation_Week11_-_R_Statistics.html
## Presentation_Week11_-_R_Statistics_files
## Presentation_Week12_-_R_Ek_Ders.Rmd
## Presentation_Week12_-_R_Ek_Ders.html
## Presentation_Week12_-_R_Ek_Ders_files
## Presentation_Week12_-_R_Probability.Rmd
## Presentation_Week12_-_R_Probability.html
## Presentation_Week12_-_R_Probability_files
## Presentation_Week13_-_R_Probability.Rmd
## Presentation_Week13_-_R_Probability.html
## Presentation_Week13_-_R_Probability_files
## Presentation_Week15_-_R_Probability.Rmd
## Presentation_Week15_-_R_Probability.html
## Presentation_Week1_-_Data_and_Code.Rmd
## Presentation_Week1_-_Data_and_Code.html
## Presentation_Week2_-_Linux_and_Python.Rmd
## Presentation_Week2_-_Linux_and_Python.html
## Presentation_Week2_-_Linux_and_Python.pdf
## Presentation_Week2_20-21_-_Linux_and_Python.Rmd
## Presentation_Week2_20-21_-_Linux_and_Python.html
## Presentation_Week3_-_Data_Sources_and_Download.Rmd
## Presentation_Week3_-_Data_Sources_and_Download.html
## Presentation_Week3_20-21_-_Data_Sources_and_Download.Rmd
## Presentation_Week3_20-21_-_Data_Sources_and_Download.html
## Presentation_Week4_-_Introduction_to_R.Rmd
## Presentation_Week4_-_Introduction_to_R.html
## Presentation_Week5_-_R_Language_Part_1.Rmd
## Presentation_Week5_-_R_Language_Part_1.html
## Presentation_Week7_-_R_Language_Part_3.Rmd
## Presentation_Week7_-_R_Language_Part_3.html
## Presentation_Week9_-_R_Programming_Part_1.Rmd
## Presentation_Week9_-_R_Programming_Part_1.html
## Presentation_Week9_-_R_Programming_Part_1_files
## R_and_R_Studio.jpeg
## R_and_R_Studio.png
## R_logo.jpeg
## Richard.jpg
## Rplot.png
## Shp_mean_temp.png
## Software_Tools_R_Homework2.Rmd
## Software_Tools_R_Homework2.html
## Software_Tools_R_Homework2.nb.html
## Software_Tools_R_Homework2.pdf
## Software_Tools_R_Homework3.Rmd
## Software_Tools_R_Homework3.nb.html
## Software_Tools_R_Homework3.pdf
## Software_Tools_R_Homework3_Answer.Rmd
## Software_Tools_R_Homework3_Answer.nb.html
## The_Book_of_R.png
## The_Book_of_R_small.png
## Tr_temp_mean.png
## VAPOR_HAIL_ANIME.gif
## Week1_rpubs.Rmd
## Week1_rpubs.html
## agu_pre.png
## ai.png
## algorithm.png
## alma.jpg
## alma_01.jpg
## alma_a.jpg
## alma_correlator.jpg
## alma_transporter.jpg
## anaconda.png
## analysis.png
## apache_point.jpg
## apply1.png
## apply_1.png
## arcgis.png
## arit_op.png
## array.png
## art_mean.png
## art_mean_a.png
## ascii_1.png
## ascii_2.png
## aybe_seminar.png
## ber_1.png
## ber_2.png
## big_data1.png
## binomial_r.png
## book_11th.png
## book_11th_b.png
## book_7th.png
## book_chp1.png
## book_cover_week5.png
## book_cover_week9.png
## book_flow.png
## book_flow_2020_21.png
## book_w12_a.png
## book_w12_b.png
## book_week5.png
## cd1.png
## cd2.png
## cdo.png
## cdo1.png
## cdo2.png
## cdo3.png
## cdo4.png
## cdo5.png
## cdo_00.png
## cdo_01.png
## clear.png
## clim_re_v.png
## code.png
## coercion.png
## coercion_mini.png
## command_line.png
## concept_array.png
## concept_array_q.png
## conda.png
## conditions_book.png
## corr_1.png
## corr_2.png
## corr_3.svg
## corr_4.png
## corr_4.svg
## corr_a.png
## corr_b.png
## course_github.png
## course_github_2020_21.png
## coursera.png
## covar_a.png
## covar_b.png
## covar_c.png
## cp.png
## cp1.png
## cran_metu.png
## cran_turkey.png
## cru.png
## cru_20-21.png
## curl_00.png
## cygwin.png
## data.csv
## data_analytics.png
## data_assim.jpeg
## data_assim_00.png
## data_frame.png
## data_manip.jpg
## data_mining.svg
## data_structure.png
## data_structure1.png
## data_structure1_array.png
## data_structure1_copy.png
## data_structure_copy.png
## data_types.png
## datacamp.png
## datacamp01.png
## datacamp1.png
## datacamp_11th.png
## datascience.png
## datashape.jpg
## datum.png
## dc1.png
## dc10.png
## dc11.png
## dc2.png
## dc3.png
## dc4.png
## dc5.png
## dc5a.png
## dc5aa.png
## dc5ab.png
## dc5ac.png
## dc6.png
## dc7.png
## dc8.png
## dc9.png
## dc_00.png
## dc_01.png
## dc_02.png
## dc_03.png
## dc_bash.png
## dc_w12.png
## deep.jpg
## dene_sill.Rmd
## dene_sill.html
## dene_sill_files
## denemepdf.docx
## denemepdf.html
## denemepdf.nb.html
## denemepdf.pdf
## dffile.csv
## dffile.txt
## download.png
## dropbox.png
## dt10w.png
## dt_13.png
## dt_conda.png
## dt_r_intro_20-21.png
## earth_v.png
## earthdata.png
## ed_20-21.png
## eda.png
## edx.png
## ek_anket.png
## ensemble.png
## eobs.png
## eobs_20-21.png
## era.png
## era_v.png
## esgf.png
## ex_syl_w3.png
## excel.png
## exit.png
## extended_4th_week.png
## extended_syll_2nd_week.png
## extended_syllabus.png
## extended_syllabus1.png
## extended_syllabus_2020_21.png
## extended_syllabus_3th_week.png
## fig.html
## fig.png
## fig_temp.png
## filer_folder.png
## filer_folder_00.png
## filer_folder_01.png
## filezil.png
## filezilla.png
## find.png
## five_number_summary.png
## forecast.png
## forecast_co2.png
## formula.png
## fz_00.png
## fz_01.png
## fz_02.png
## fz_03.png
## generate.png
## gfs.png
## gfs_v.png
## github.png
## github1.png
## github2.png
## github3.png
## github4.png
## gnu_logo.png
## gnu_logo_small.png
## grib.jpg
## grib_1.png
## grid_diff.jpg
## grid_sample.jpg
## gridded.jpg
## hdf5_structure.jpg
## help.png
## hist_5.png
## hist_gg.png
## history.png
## hw_quiz_flow_2020_21.png
## if1.png
## if1a.png
## if1b.png
## if1c.png
## if2.png
## if2a.png
## if3.png
## if3a.png
## if3b.png
## if3c.png
## if3d.png
## integral_fig.png
## integral_fig1.png
## iot.png
## ipcc_res.png
## july_pre.png
## jupyter.png
## jupyter_notebook.png
## kaho.png
## kernel.jpg
## kernel_00.jpg
## kernerl_01.png
## kernerl_02.png
## khanacademy.png
## knmi.png
## knmi_20-21.png
## knmi_20-21_00.png
## knmi_20-21_01.png
## knmi_20-21_02.png
## knmi_20-21_03.png
## knmi_20-21_04.png
## languages.png
## lapply2.png
## last_week.png
## last_week_2nd.png
## linus.jpeg
## linux_dist.png
## linux_logo.png
## list0.png
## list2.png
## list_1.jpg
## logic_op.png
## machine.jpg
## mat1.jpg
## mat1.png
## matrice_cut.png
## matrices.png
## matrices1.png
## mauna_loa.png
## median.png
## median_a.png
## mendeley.png
## metadata0.png
## metadata00.png
## metadata02.png
## metadata1.png
## metadata1a.png
## meted.png
## meteo_earth.png
## mining.jpg
## mining1.jpg
## mkdir1.png
## mkdir2.png
## mod.png
## model.png
## moto_bike.png
## mv.png
## my_notebook.png
## my_profile
## my_r_notebook.png
## my_r_notebook_1.png
## my_r_notebook_html.png
## my_r_notebook_pdf.png
## my_r_notebook_word.png
## my_r_team_invite.pdf
## my_r_team_invite.png
## mynewfile.png
## nc.png
## nc_open_a.png
## nc_open_b.png
## ncdf4_a.png
## ncl.png
## ncl0.png
## ncl1.png
## ncl2.png
## ncl_00.png
## ncl_01.png
## ncl_02.png
## ncl_03.png
## ncl_04.png
## ncll.png
## nco.png
## nco_diff.png
## ncview.png
## nested_grid.jpg
## netcdf.png
## netcdf_1.png
## new_data.csv
## noaa.png
## noaa_01.png
## noaa_02.png
## noaa_03.png
## noaa_04.png
## noaa_04a.png
## noaa_04b.png
## noaa_04c.png
## noaa_04d.png
## noaa_04e.png
## noaa_05.png
## noaa_06.png
## noaa_07.png
## noaa_earth.png
## normal.png
## normal_1.png
## normal_2.png
## normal_3.png
## nwp_1.png
## nwp_2.png
## observation_data.png
## orcid.png
## os.png
## overleaf.png
## page_7th.png
## page_week5.png
## panoply.png
## panoply_00.png
## pnply_a.png
## pnply_b.png
## poisson_r.png
## pop_sample.png
## practice_1_w5.png
## practice_func.png
## prepie.png
## printenv.png
## pwd_mac.png
## pwd_mac1.png
## pwd_win.png
## python.jpg
## python_term.png
## qgis.png
## qnap.jpeg
## qrt.png
## r-for-loop.png
## r-for1.png
## r-for2.png
## r-loops.png
## r-programming-data-types.png
## r-repeat-loop.png
## r-while-loop.png
## r_book_week5.png
## r_classic1.png
## r_classic2.png
## r_clust.jpg
## r_comp.png
## r_corr.png
## r_dplyr.png
## r_files.png
## r_inter.png
## r_linear.png
## r_markdown.png
## r_screen1.png
## r_screen10.png
## r_screen11.png
## r_screen12.png
## r_screen13.png
## r_screen14.png
## r_screen15.png
## r_screen16.png
## r_screen17.png
## r_screen18.png
## r_screen19.png
## r_screen2.png
## r_screen20.png
## r_screen21.png
## r_screen22.png
## r_screen23.png
## r_screen24.png
## r_screen25.png
## r_screen3.png
## r_screen4.png
## r_screen5.png
## r_screen6.png
## r_screen7.png
## r_screen8.png
## r_screen9.png
## r_script_w5.png
## r_shiny.png
## r_shiny1.png
## r_storms.gif
## r_team_members.pdf
## r_team_members.png
## r_team_pending.pdf
## r_team_pending.png
## r_terminal.png
## r_time.gif
## r_visual.png
## r_web.png
## rapor_00.png
## rapor_01.png
## raster_0.gif
## raster_dataset.png
## raster_vs_vector.png
## rcsv.png
## rdelim.png
## reanalysis.jpg
## res_spatial.gif
## researchgate.png
## rid1.png
## rid2.png
## rid3.png
## rid4.png
## rm.png
## rncdf_a.png
## robert_gentleman.jpg
## root.png
## root_fig.gif
## ross_lhaka.jpg
## rsconnect
## rstudio.png
## rstudio_cloud.png
## rstudio_down.png
## rstudio_logo.png
## rstudio_product.png
## rstudio_ubuntu.png
## rtb1.png
## rtb2.png
## sample_vs_pop.png
## sc_00.png
## sci_math.png
## sd1.png
## sd2.png
## shape_r.png
## shell_00.png
## shell_01.png
## shp.png
## shp_mask.png
## shp_tr_mean.png
## sil_notebook.Rmd
## sil_notebook.html
## sil_notebook.nb.html
## sil_notebook_files
## sil_rmarkdown.Rmd
## sil_rmarkdown.html
## sil_rmarkdown_files
## sil_sweave-concordance.tex
## sil_sweave.Rnw
## sil_sweave.log
## sil_sweave.tex
## simulation.jpg
## slide_in_r.png
## sly_20-21_3rd.png
## somenewfile.txt
## split_screen.png
## stackoverflow.png
## sublimetext.png
## summary_a.png
## summary_b.png
## summary_c.gif
## syl_w12.png
## syl_w4_20-21.png
## syllabus.png
## syllabus7_son.png
## syllabus_11th.png
## syllabus_13.png
## syllabus_20-21_1st_week.png
## syllabus_20-21_2nd_week.png
## syllabus_20-21_3rd_week.png
## syllabus_4th_week.png
## syllabus_5th.png
## syllabus_7th.png
## syllabus_9.png
## syllabus_w6.png
## syllabus_week5.png
## teamviewer.png
## term_00.png
## term_01.jpg
## terminal.png
## terminal0.png
## terminal1.png
## th_1.gif
## th_1.png
## th_2.gif
## th_2.jpg
## th_3.gif
## touch.png
## udemy.png
## udemy1.png
## udemy_20-21.png
## udemy_content_1.png
## udemy_hm1.png
## unif_a.png
## unif_b.png
## unix_develop.jpg
## unix_linux.png
## unix_pl.jpg
## var1.png
## var2.png
## var3.png
## vec_ras.jpg
## vec_rep.png
## vector-raster.gif
## vector.png
## vector1a.png
## vector1b.png
## vector_type.png
## vector_type_1.jpg
## vector_vs_raster.png
## vi_0.png
## vi_00.png
## vi_1.png
## vi_2.png
## vi_3.png
## visual.jpg
## visual_2.jpg
## w15_anket.png
## w15_b1.png
## w15_b2.png
## w15_d1.png
## w15_d1a.png
## w15_d2.png
## w15_d2a.png
## w15_mat.png
## w15_sy.png
## w4_ex_sly.png
## warning.png
## wc_01_20-21.png
## wc_20-21_02.png
## web_in_r.png
## webminal.png
## week-book.png
## week10.Rmd
## week10.html
## week10.png
## week100.png
## week10_book.png
## week11.Rmd
## week11.html
## week13.Rmd
## week13.html
## week2_sil.Rmd
## week2_sil.html
## week2_sil.log
## week2_sil.tex
## week3.Rmd
## week3.html
## week4.Rmd
## week4.html
## week4_extended_syllabus.png
## week5.Rmd
## week5.html
## week7.Rmd
## week7.html
## week9.Rmd
## week9.html
## weight_height.txt
## wetransfer.png
## wget.jpg
## wget_00.png
## what_data.svg
## win_folder.png
## windy_v.png
## wolfram-alpha.png
## wordclim.png
## wp_week3.png
## zar_2.png
## zar_a.png
## zenodo-doi.png

Directory Commands - pwd and ls

Workind Directory (or Path), files and folders

Directory Commands - cd

(Change Directory)

cd Presentation/

Double Left Click

Directory Commands - mkdir

(Make Directory)

mkdir <new_folder_name>

Right Click -> New Folder

File Commands

• touch

• cat (Concatenate)

• rm (Remove)

• cp (Copy)

• mv (Move)

File Commands - touch

touch <my_new_file>

Rigth Click -> New -> New File (no extension like .txt)

File Commands - cat

(Concatenate)

cat my_new_file

This is my new file. Hi!

Show inside file

File Commands - cp

(Copy)

cp my_new_file my_new_file2

Right Click -> Copy and Paste, (with Rename)

File Commands - mv

(Move)

mv my_new_file2 my_new_file3

Right Click -> Cut and Paste (or Rename)

File Commands - rm

(Remove)

rm my_new_file my_new_file3

Right Click -> Delete

Special Commands

• find

• help

• history

• clear

• date and cal

• exit

Special Commands - find

find -name <name_of_file>

Search Bar

Special Commands - help

find --help

How to use and information, for a command

Special Commands - history

history

Special Commands - clear

clear

Special Commands - date and cal

date

## Fri Nov  6 16:35:56 +03 2020

cal

##    November 2020      
## Su Mo Tu We Th Fr Sa  
##  1  2  3  4  5 _ _6  7  
##  8  9 10 11 12 13 14  
## 15 16 17 18 19 20 21  
## 22 23 24 25 26 27 28  
## 29 30                 
## 

Special Commands - exit

exit

vi (Visual) Editor

• vi editor is a screen-oriented text editor originally created for the Unix operating system. (we can also use in Unix-like systems). You can save and run you code

• It works in terminal, (so looks similar with terminal)

vi Editor and Print Commands

• vi

• esc (default mode)

• i (insert mode)

• :q (just quit)

• :q! (don’t save and quit)

• :qw (write/save and quit)

• grep and echo

• head and tail

• sed (stream editor)

vi Editor and Print Commands - vi

go to webminal.org

vi Editor and Print Commands - esc

(Default Mode)

vi Editor and Print Commands - i

(Insert Mode)

vi Editor and Print Commands - :wq

(Write/Save and Quit)

vi Editor and Print Commands - grep and echo

cat my_profile

grep my_profile

grep ITU my_profile

echo my_profile

name=Emir

echo $name

cat shows the inside

grep is searching for something

echo just prints it directly (or logically)

we can assign someting with ‘=’ basically

vi Editor and Print Commands - head and tail

head my_profile

tail my_profile

head shows first ten rows

tail shows last ten rows

vi Editor and Print Commands - sed

(Stream Editor)

Replacing or substituting string;

sed 's/ITU/ODTU/' my_profile

sed '5d' my_profile 

cat my_profile

sed, just prints it as rewrite

Symbols

• | (and)
• > (assing)
• $ (special variable)
• ? (an unknown character)
• * (an unknown sroup of characters)

cat my_profile | sort

ls > my_list

x=3
echo $x

ls my*

ls ?y_list* 

Script

• script is a text of codes, consist of tasks

• script can work as computer programs or every where every time

• shell works with script (shell script)

echo $SHELL

Bash Script

touch my_bash_script.sh
vi my_bash_script.sh

x=5
y=3
echo $((x+y))

bash my_bash_script.sh

8

Practice

1. Learn where you are (Print your working directory)
2. Look at inside (list all documents and directories)
3. Create a new folder (make a directory,<my_new_dir>)
4. Go to the <my_new_dir> (change your directory)
5. Create a new file (touch it, file name : <my_new_file>)
6. Open this new file and write your name (vi-insert mode)
7. Save your work and close the file (write + quit)
8. Print your name on the screen (grep, tail, head, cat)
9. Put <my_new_file> at the parent directory (move it)
10. Go to parent directory (change directory with two dots)
11. Create a copy, name; <my_new_file_2>
12. Remove your first folder <my_new_dir>
13. List all documents and directories

Quiz

Rules

• You will see the question and answer options on the screen
• You have to choise your answer it in your device
• You will have 5 or 10 second to answer for each
• There are just two type questions:
• 1. True and False type (two options)
• 2. Quiz type (four different options)
• Higher score for speed and correct answer
• You don’t have to use your real name

Quiz

Ex for True and False type

Quiz

Introduction to Gnu/Linux

Go to kahoot.it

LINK

What is the Python

• Python is an interpreted, high-level and general-purpose programming language.
• Created by Guido van Rossum and first released in 1991.
• Python 2.0, released 2000, Python 3.0, released 2008.
• Latest stable version is 3.8.3 (May 14, 2020)
• Zen of Python; Beautiful, Explicit, Simple, Readability

Python in Terminal

webminal.org

GCC : GNU Compiler Collection

Python Script

vi new.py                     

x=5+3
print(x)
print('i did it')

python new.py

8

What is the Anaconda/Jupyter

Python in Anaconda/Jupyter

jupyter notebook

Next Week

• Data Fortmats, Sources and Download

• NCL, nco, cdo